Variant report

Variant	rs12616953
Chromosome Location	chr2:145794405-145794406
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10496971	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10496972	0.80[ASN][1000 genomes]
rs11689317	0.80[AMR][1000 genomes]
rs12618061	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12990539	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12990953	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13001583	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13004410	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13009916	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13010262	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13033869	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1371047	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16824386	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1898732	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2381685	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34409381	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34985138	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4662413	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56014517	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67431032	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs67969609	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7561039	0.80[ASN][1000 genomes]
rs7575637	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002563	chr2:145182201-145863253	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv535957	chr2:145182201-145863253	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv932113	chr2:145515124-145844491	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv834398	chr2:145659419-145830156	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv431768	chr2:145741527-145981491	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:145787800-145794600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:145789200-145802400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:145793400-145795000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:145793600-145795000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:145793800-145794800	Active TSS	NHLF	lung
6	chr2:145794000-145794600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:145794000-145794600	Active TSS	Osteobl	bone
8	chr2:145794000-145794800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr2:145794000-145794800	Active TSS	Right Atrium	heart
10	chr2:145794000-145795000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:145794000-145795600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:145794000-145795600	Active TSS	Brain Anterior Caudate	brain
13	chr2:145794000-145795600	Active TSS	HSMMtube	muscle
14	chr2:145794200-145794800	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr2:145794200-145794800	Flanking Active TSS	Fetal Lung	lung
16	chr2:145794200-145794800	Active TSS	Ovary	ovary
17	chr2:145794200-145795000	Active TSS	A549	lung
18	chr2:145794200-145795200	Active TSS	NHDF-Ad	bronchial
19	chr2:145794200-145796000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:145794400-145794600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:145794400-145794600	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr2:145794400-145794600	Active TSS	Brain Substantia Nigra	brain
23	chr2:145794400-145794800	Active TSS	Adipose Nuclei	Adipose
24	chr2:145794400-145795400	Active TSS	Brain Hippocampus Middle	brain
25	chr2:145794400-145795600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:145794400-145795600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:145794400-145796200	Enhancers	HSMM	muscle

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